Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_012469084.1 GLOV_RS04980 glutamate 5-kinase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000020385.1:WP_012469084.1 Length = 376 Score = 153 bits (387), Expect = 1e-41 Identities = 98/275 (35%), Positives = 148/275 (53%), Gaps = 19/275 (6%) Query: 8 RAFARDVKRIVVKVGTAVVTGKGGRLALGRLGALCEQLAELNSDGFEVILVSSGAVGLGR 67 R + V+R+V+KVG+ V+T +GG L + LC+++A L G EVILVSSGAV GR Sbjct: 3 RGLLQQVRRVVIKVGSRVLTVEGGGLDYDAISRLCDEMAGLRQQGIEVILVSSGAVAAGR 62 Query: 68 QRLRYRQLVNSSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVNDSS 127 LR S+ L PQ + A A VGQ LM Y+ + + AQ+L+ Sbjct: 63 DALR------SADTTLTIPQKQ----AAAAVGQPLLMQAYQQACTRHGLVTAQILLTAED 112 Query: 128 FRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALEL 187 +++ T++++L +P+ NEND+++ F DND+L+AL+ Sbjct: 113 LANRNRFLNARTTLEALLTAGALPVINENDSVAVAEIK-------FGDNDNLSALVTSLA 165 Query: 188 KADLLILLSDVEGLYT-GPPSDPNSKLIHTFVK-EKHQDEITFGDKSRLGRGGMTAKVKA 245 +ADLL++L+D+EGLY+ P SDP+++LI + + + G S +G GGM KV A Sbjct: 166 EADLLLILTDIEGLYSANPASDPDAELIPLVRSITREIERMAGGSGSNVGTGGMATKVTA 225 Query: 246 AVNAAYAGIPVIITSGYSAENIDKVLRGLRVGTLF 280 A AA G+P I+ G I + G +GTLF Sbjct: 226 AKKAARFGVPTILAPGKQPGVITAAVSGQEIGTLF 260 Lambda K H 0.318 0.135 0.378 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 497 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 717 Length of database: 376 Length adjustment: 35 Effective length of query: 682 Effective length of database: 341 Effective search space: 232562 Effective search space used: 232562 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory